Hi Fokes,
I've checked all the usual TX/RX reversal, 5V or 3.3V, RTS, DTR, board type and auto reset hardware, havn't got to the root cause yet, but going back to an older bootloader does work. I do think it is related to reset, and as some has suggested try a manual reset, however I found it very difficult to get the timing correct for it the work.
I have come to this conclusion because I an able to program an Arduino Mini Pro 5V with the FTDI lead and b'board, I checked the b'loader version on said Mini Pro using a sketch, reprogrammed the clone with the same b'loader and it works reliably.
So I'm convinced it's b'loader based, may be the root is due to some acknowledgement signal or timing etc. It seems that OPTIbootloaded and the FTDI Chip are not compatible, (handshaking etc, hardware is not a problem). The UNO uses a 8U2 device with a build-in USB controller. If someone is interested in using a clone UNO I would suggest buying a, https://www.sparkfun.com/products/10277, a 8U2 b'board, this should work without problems.
When I have time I will investigate further, may even buy the above.
ATB Dan, living and learning:-)